RTCB_BRAFL
ID RTCB_BRAFL Reviewed; 507 AA.
AC C3YN79;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 28-JUL-2009, sequence version 1.
DT 03-AUG-2022, entry version 61.
DE RecName: Full=RNA-splicing ligase RtcB homolog {ECO:0000255|HAMAP-Rule:MF_03144};
DE EC=6.5.1.8 {ECO:0000255|HAMAP-Rule:MF_03144};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000255|HAMAP-Rule:MF_03144};
GN ORFNames=BRAFLDRAFT_216547;
OS Branchiostoma floridae (Florida lancelet) (Amphioxus).
OC Eukaryota; Metazoa; Chordata; Cephalochordata; Leptocardii; Amphioxiformes;
OC Branchiostomidae; Branchiostoma.
OX NCBI_TaxID=7739;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S238N-H82; TISSUE=Testis;
RX PubMed=18563158; DOI=10.1038/nature06967;
RA Putnam N.H., Butts T., Ferrier D.E.K., Furlong R.F., Hellsten U.,
RA Kawashima T., Robinson-Rechavi M., Shoguchi E., Terry A., Yu J.-K.,
RA Benito-Gutierrez E.L., Dubchak I., Garcia-Fernandez J., Gibson-Brown J.J.,
RA Grigoriev I.V., Horton A.C., de Jong P.J., Jurka J., Kapitonov V.V.,
RA Kohara Y., Kuroki Y., Lindquist E., Lucas S., Osoegawa K., Pennacchio L.A.,
RA Salamov A.A., Satou Y., Sauka-Spengler T., Schmutz J., Shin-I T.,
RA Toyoda A., Bronner-Fraser M., Fujiyama A., Holland L.Z., Holland P.W.H.,
RA Satoh N., Rokhsar D.S.;
RT "The amphioxus genome and the evolution of the chordate karyotype.";
RL Nature 453:1064-1071(2008).
CC -!- FUNCTION: Catalytic subunit of the tRNA-splicing ligase complex that
CC acts by directly joining spliced tRNA halves to mature-sized tRNAs by
CC incorporating the precursor-derived splice junction phosphate into the
CC mature tRNA as a canonical 3',5'-phosphodiester. May act as an RNA
CC ligase with broad substrate specificity, and may function toward other
CC RNAs. {ECO:0000255|HAMAP-Rule:MF_03144}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho-
CC ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA +
CC diphosphate + GMP; Xref=Rhea:RHEA:68076, Rhea:RHEA-COMP:10463,
CC Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83062,
CC ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03144};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end
CC dephospho-ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl-
CC ribonucleotide-RNA + diphosphate + GMP + H(+); Xref=Rhea:RHEA:68080,
CC Rhea:RHEA-COMP:10464, Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83064,
CC ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03144};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03144};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03144};
CC -!- SUBUNIT: Catalytic component of the tRNA-splicing ligase complex.
CC {ECO:0000255|HAMAP-Rule:MF_03144}.
CC -!- MISCELLANEOUS: Ligation probably proceeds through 3 nucleotidyl
CC transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to
CC 3'-P termini in a step that precedes 3'-P activation with GMP. In the
CC first nucleotidyl transfer step, RTCB reacts with GTP to form a
CC covalent RTCB-histidine-GMP intermediate with release of PPi; in the
CC second step, the GMP moiety is transferred to the RNA 3'-P; in the
CC third step, the 5'-OH from the opposite RNA strand attacks the
CC activated 3'-P to form a 3',5'-phosphodiester bond and release GMP.
CC {ECO:0000255|HAMAP-Rule:MF_03144}.
CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000255|HAMAP-
CC Rule:MF_03144}.
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DR EMBL; GG666533; EEN58185.1; -; Genomic_DNA.
DR RefSeq; XP_002602173.1; XM_002602127.1.
DR AlphaFoldDB; C3YN79; -.
DR SMR; C3YN79; -.
DR STRING; 7739.XP_002602173.1; -.
DR eggNOG; KOG3833; Eukaryota.
DR InParanoid; C3YN79; -.
DR OrthoDB; 394775at2759; -.
DR Proteomes; UP000001554; Partially assembled WGS sequence.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0072669; C:tRNA-splicing ligase complex; IBA:GO_Central.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IBA:GO_Central.
DR GO; GO:0000971; P:tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate; IBA:GO_Central.
DR Gene3D; 3.90.1860.10; -; 1.
DR HAMAP; MF_03144; RtcB_euk; 1.
DR InterPro; IPR001233; RtcB.
DR InterPro; IPR036025; RtcB-like_sf.
DR InterPro; IPR027513; RtcB_euk.
DR PANTHER; PTHR11118; PTHR11118; 1.
DR Pfam; PF01139; RtcB; 1.
DR SUPFAM; SSF103365; SSF103365; 1.
DR PROSITE; PS01288; UPF0027; 1.
PE 3: Inferred from homology;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..507
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000407221"
FT ACT_SITE 430
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 121
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 124
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 124
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 228..232
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 229
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 261
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 355..356
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 355
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 404..407
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 411
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 430..433
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 506
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ SEQUENCE 507 AA; 55759 MW; 0DFF75A8A1BE4BAD CRC64;
MPENRSYNDE LNFLDKIDAN TWRIKKGFVP NMKVDGFFYV NDLLEKLMFD ELRQHSRAAG
FGGFLPAMKQ IANVAALPGI VQKSVGLPDV HAGYGFAIGN LAAFDMSNPE AVVSPGGVGF
DINCGVRLLR TNLDERDVQP VKDELAQAMF DHIPVGVGSK GVIPMGARDL EEALEMGVDW
SLREGYAWAE DKEHCEEYGR MLNADQSAVG SKAKKRGLPQ LGTLGAGNHY AEIQVVDEIF
DDYASQRMGI DHKGQVVVMI HSGSRGFGHQ VATDALVAME KAMKRDKVLT NDRQLACARI
HSPEGQEYLK GMACAANFAW VNRSSMTFLS RQAFAKVFNT TPDDLDMQLI YDVSHNIAKM
EEHISFQLST TLLVHRKGST RAFPPHHPLI PVDYQLSGQP VLIGGTMGTC SYVLTGTEKG
MEQTFGTTCH GAGRAWSRAK SRRNLDYQEV LDRLAELGIS IRVASPKLVM EEAPESYKNV
TDVVNTCHAV GISKKAIKLR PIAVIKG
